Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 245 bits (625), Expect = 2e-69 Identities = 132/295 (44%), Positives = 183/295 (62%), Gaps = 4/295 (1%) Query: 4 VTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLID 63 +T ++ K + ++ L + +GEF +GPSGCGK+TLLR++AG E T G +LID Sbjct: 15 ITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILID 74 Query: 64 NQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQL 123 Q ++++PP R V MVFQSYA++PHMTVA+N+A+GLK+ +V K E + RV E++QL Sbjct: 75 GQDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALELVQL 134 Query: 124 DKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRI 183 L RKP LSGGQRQRVA+ R +V+ P+V L DEPLS LDA LR QMR E+ L +++ Sbjct: 135 GGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCTLQEKV 194 Query: 184 RSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVE 243 T I VTHDQ EA+ LA + V++ G + QV P LY +P +RFVA F+G Q+N E Sbjct: 195 GITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIG--QVNLFE 252 Query: 244 VRAISASPETVTIELPSGYPLTLPVDGSAVSP-GDPLTLGIRPEHFVMPDEADFT 297 P I+ P P+ + +D P G + IRPE + +AD T Sbjct: 253 GVLAVDEPSHAVIKSPD-LPVDIFLDHGVTGPRGGTVWAAIRPEKIELHKKADDT 306 Lambda K H 0.322 0.139 0.405 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 332 Number of extensions: 14 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 371 Length of database: 381 Length adjustment: 30 Effective length of query: 341 Effective length of database: 351 Effective search space: 119691 Effective search space used: 119691 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory